Evidence map›Paper›PMID 34180992›Full record

ArticleGenome biology and evolution2021

Unexpected Discovery of Hypermutator Phenotype Sounds the Alarm for Quality Control Strains.

Kun Wu, Zhou-Hua Cheng, Emily Williams, Nathan T Turner, Dapeng Ran, Haichao Li, Xia Zhou, Huilin Guo, Way Sung, Dong-Feng Liu and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Kun WuInstitute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China.
Zhou-Hua ChengCAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China.
Emily WilliamsCenter for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
Nathan T TurnerDepartment of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA.
Dapeng RanInstitute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China.
Haichao LiInstitute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China.
Xia ZhouInstitute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China.
Huilin GuoInstitute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China.
Way SungDepartment of Bioinformatics and Genomics, University of North Carolina, Charlotte, North Carolina, USA.ORCID 0000-0002-8336-8913
Dong-Feng LiuCAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China.
Michael LynchCenter for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
Hongan LongInstitute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, China.

Funding

Causes and Population-genetic Consequences of Molecular VariationR35GM122566 · NIGMS · TRUSTEES OF INDIANA UNIVERSITY · PI Michael R LYNCH · 2017 to 2026
$7.7M
The Rate and Molecular Spectrum of Spontaneous MutationsR01GM036827 · NIGMS · UNIVERSITY OF OREGON · PI LYNCH, MICHAEL R · 1988 to 2016
$5.7M
NIGMS NIH HHS R01 GM036827NIGMS NIH HHS R35 GM122566
6 · The paper itself

Abstract

Microbial strains with high genomic stability are particularly sought after for testing the quality of commercial microbiological products, such as biological media and antibiotics. Yet, using mutation-accumulation experiments and de novo assembled complete genomes based on Nanopore long-read sequencing, we find that the widely used quality-control strain Shewanella putrefaciens ATCC-8071, also a facultative pathogen, is a hypermutator, with a base-pair substitution mutation rate of 2.42 × 10-8 per nucleotide site per cell division, ∼146-fold greater than that of the wild-type strain CGMCC-1.6515. Using complementation experiments, we confirm that mutL dysfunction, which was a recent evolutionary event, is the cause for the high mutation rate of ATCC-8071. Further analyses also give insight into possible relationships between mutation and genome evolution in this important bacterium. This discovery of a well-known strain being a hypermutator necessitates screening the mutation rate of bacterial strains before any quality control or experiments.

Indexed as

Anti-Bacterial AgentsMutation RateMutationPhenotypeQuality ControlAnti-Bacterial Agentscomparative genomicsDNA mismatch repairgenome evolutionmutation spectrumShewanella

Identifiers

PMID34180992
PMCPMC8350357

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.